Multiple sequence alignment - TraesCS7D01G326600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G326600 chr7D 100.000 3576 0 0 1 3576 417036788 417033213 0.000000e+00 6604.0
1 TraesCS7D01G326600 chr7D 100.000 119 0 0 3457 3575 3777884 3777766 1.670000e-53 220.0
2 TraesCS7D01G326600 chr7B 90.829 1363 96 10 5 1352 432934825 432933477 0.000000e+00 1797.0
3 TraesCS7D01G326600 chr7B 90.605 1224 83 8 1853 3068 432932918 432931719 0.000000e+00 1594.0
4 TraesCS7D01G326600 chr7B 95.427 328 10 2 1494 1820 432933241 432932918 5.290000e-143 518.0
5 TraesCS7D01G326600 chr7B 89.086 394 34 4 3065 3453 432931668 432931279 6.940000e-132 481.0
6 TraesCS7D01G326600 chr7A 90.616 1364 97 15 5 1352 481691233 481689885 0.000000e+00 1781.0
7 TraesCS7D01G326600 chr7A 91.496 1223 74 10 1853 3068 481689404 481688205 0.000000e+00 1655.0
8 TraesCS7D01G326600 chr7A 91.228 399 27 4 3065 3459 481688154 481687760 1.460000e-148 536.0
9 TraesCS7D01G326600 chr7A 92.147 382 21 5 1447 1820 481689784 481689404 6.800000e-147 531.0
10 TraesCS7D01G326600 chr6D 100.000 121 0 0 3456 3576 433247065 433246945 1.290000e-54 224.0
11 TraesCS7D01G326600 chr5D 100.000 120 0 0 3457 3576 537766374 537766493 4.650000e-54 222.0
12 TraesCS7D01G326600 chr4D 100.000 120 0 0 3457 3576 471296676 471296557 4.650000e-54 222.0
13 TraesCS7D01G326600 chr2D 100.000 120 0 0 3457 3576 484886438 484886557 4.650000e-54 222.0
14 TraesCS7D01G326600 chr2D 99.174 121 1 0 3456 3576 576917546 576917666 6.010000e-53 219.0
15 TraesCS7D01G326600 chr2D 99.174 121 1 0 3456 3576 645623189 645623069 6.010000e-53 219.0
16 TraesCS7D01G326600 chr1D 100.000 120 0 0 3457 3576 423023473 423023354 4.650000e-54 222.0
17 TraesCS7D01G326600 chr1D 90.566 53 5 0 2935 2987 138272018 138272070 1.780000e-08 71.3
18 TraesCS7D01G326600 chr3D 98.374 123 2 0 3454 3576 560035343 560035465 2.160000e-52 217.0
19 TraesCS7D01G326600 chr1B 92.453 53 4 0 2935 2987 213329016 213328964 3.830000e-10 76.8
20 TraesCS7D01G326600 chr2A 88.235 51 6 0 2944 2994 652774783 652774733 1.070000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G326600 chr7D 417033213 417036788 3575 True 6604.00 6604 100.00000 1 3576 1 chr7D.!!$R2 3575
1 TraesCS7D01G326600 chr7B 432931279 432934825 3546 True 1097.50 1797 91.48675 5 3453 4 chr7B.!!$R1 3448
2 TraesCS7D01G326600 chr7A 481687760 481691233 3473 True 1125.75 1781 91.37175 5 3459 4 chr7A.!!$R1 3454

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
224 230 0.030101 ACGGGCATTCAACAACGTTG 59.970 50.0 26.20 26.20 0.0 4.10 F
887 898 0.250038 GTGTGTGCTTCTGAGGCTCA 60.250 55.0 17.68 17.68 0.0 4.26 F
1904 2061 0.179097 GCTTCAACTAGGGGAGCTCG 60.179 60.0 7.83 0.00 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 1061 0.108281 GGTTCTACTTCTCACGGGGC 60.108 60.0 0.0 0.0 0.0 5.80 R
1945 2102 0.468226 AGAAGGCACCAACTTGACGA 59.532 50.0 0.0 0.0 0.0 4.20 R
3463 3687 0.032952 AAAACGTCGCACAGGAGCTA 59.967 50.0 0.0 0.0 0.0 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.017109 AGGATTATTGAAACACGTGATATGCC 60.017 38.462 25.01 12.31 0.00 4.40
62 63 4.418013 TGAAACACGTGATATGCCTTTG 57.582 40.909 25.01 0.00 0.00 2.77
136 142 2.119801 AGCCAATGCGAAGAACTCAT 57.880 45.000 0.00 0.00 44.33 2.90
143 149 3.333029 TGCGAAGAACTCATCCATTCA 57.667 42.857 0.00 0.00 0.00 2.57
158 164 1.739466 CATTCATGGTCCACAGAACCG 59.261 52.381 10.02 2.91 39.81 4.44
166 172 1.067776 GTCCACAGAACCGGTCTACAG 60.068 57.143 8.04 2.23 33.56 2.74
183 189 5.580297 GTCTACAGATGCCAAGAAGAAGAAG 59.420 44.000 0.00 0.00 0.00 2.85
192 198 4.503296 GCCAAGAAGAAGAAGAGGTACACA 60.503 45.833 0.00 0.00 0.00 3.72
200 206 4.875561 AGAAGAGGTACACAGGAAGTTC 57.124 45.455 0.00 0.00 0.00 3.01
201 207 3.579151 AGAAGAGGTACACAGGAAGTTCC 59.421 47.826 14.54 14.54 36.58 3.62
205 211 0.038892 GTACACAGGAAGTTCCGCGA 60.039 55.000 16.31 0.00 42.75 5.87
222 228 1.837538 CGACGGGCATTCAACAACGT 61.838 55.000 0.00 0.00 37.26 3.99
224 230 0.030101 ACGGGCATTCAACAACGTTG 59.970 50.000 26.20 26.20 0.00 4.10
279 285 3.157252 GCTCCAGCTCCATCCGGA 61.157 66.667 6.61 6.61 39.79 5.14
345 351 3.264450 ACAAGGGGAACGATCTGAATCTT 59.736 43.478 0.00 0.00 0.00 2.40
365 371 4.479796 TCTTTCCATCATCCCTCATTTCCT 59.520 41.667 0.00 0.00 0.00 3.36
366 372 3.870538 TCCATCATCCCTCATTTCCTG 57.129 47.619 0.00 0.00 0.00 3.86
416 422 1.298014 CTCCTGAGTGGGTGAAGGC 59.702 63.158 0.00 0.00 36.20 4.35
486 492 2.905959 TCGAGCGTCGAAACAATCTA 57.094 45.000 7.48 0.00 46.90 1.98
499 505 3.944055 ACAATCTACTTGAGCGTGTCT 57.056 42.857 0.00 0.00 38.29 3.41
513 519 4.579869 AGCGTGTCTTGGTTGAGATTTAT 58.420 39.130 0.00 0.00 0.00 1.40
543 549 2.429610 GGGCATCAGCTCATTGAACATT 59.570 45.455 0.00 0.00 42.33 2.71
615 621 2.425592 CACGGCAAGACCCTGTCA 59.574 61.111 0.00 0.00 34.60 3.58
619 625 0.824109 CGGCAAGACCCTGTCAGATA 59.176 55.000 0.00 0.00 34.60 1.98
681 687 0.803768 CAGTTGAGAGATCACCGGCG 60.804 60.000 0.00 0.00 0.00 6.46
700 706 1.304282 CCCAATGTGGAGTGAGGGG 59.696 63.158 0.00 0.00 40.96 4.79
750 761 5.844396 CGAAAAATAGAAAGGTTGACGTGAC 59.156 40.000 0.00 0.00 0.00 3.67
805 816 4.985538 TGTATGAAACAAACCAAACCGT 57.014 36.364 0.00 0.00 34.29 4.83
887 898 0.250038 GTGTGTGCTTCTGAGGCTCA 60.250 55.000 17.68 17.68 0.00 4.26
894 905 2.011046 GCTTCTGAGGCTCATGTGTCC 61.011 57.143 19.11 1.16 0.00 4.02
895 906 1.554160 CTTCTGAGGCTCATGTGTCCT 59.446 52.381 19.11 9.55 0.00 3.85
896 907 0.900421 TCTGAGGCTCATGTGTCCTG 59.100 55.000 19.11 3.60 0.00 3.86
1049 1061 2.024871 GTCGCATCCTCGTCTCCG 59.975 66.667 0.00 0.00 0.00 4.63
1313 1338 2.991250 GGCTCTTTGTGCCTCTGATAA 58.009 47.619 3.71 0.00 46.38 1.75
1319 1344 6.349611 GCTCTTTGTGCCTCTGATAAAATTCA 60.350 38.462 0.00 0.00 0.00 2.57
1329 1354 8.299570 GCCTCTGATAAAATTCACTCTTGAAAA 58.700 33.333 0.00 0.00 45.01 2.29
1352 1377 2.029649 TGCTTTGCTTCTTTGGCTGATC 60.030 45.455 0.00 0.00 0.00 2.92
1359 1408 2.028420 TCTTTGGCTGATCGACATGG 57.972 50.000 0.00 0.00 0.00 3.66
1363 1412 2.528743 GGCTGATCGACATGGTGCG 61.529 63.158 0.00 0.00 0.00 5.34
1382 1431 2.599848 GCGCAAATATTAGTCTGTGCCG 60.600 50.000 0.30 4.45 38.95 5.69
1383 1432 2.863740 CGCAAATATTAGTCTGTGCCGA 59.136 45.455 2.74 0.00 0.00 5.54
1384 1433 3.308595 CGCAAATATTAGTCTGTGCCGAA 59.691 43.478 2.74 0.00 0.00 4.30
1385 1434 4.201773 CGCAAATATTAGTCTGTGCCGAAA 60.202 41.667 2.74 0.00 0.00 3.46
1386 1435 5.636837 GCAAATATTAGTCTGTGCCGAAAA 58.363 37.500 0.00 0.00 0.00 2.29
1387 1436 6.265577 GCAAATATTAGTCTGTGCCGAAAAT 58.734 36.000 0.00 0.00 0.00 1.82
1388 1437 7.414436 GCAAATATTAGTCTGTGCCGAAAATA 58.586 34.615 0.00 0.00 0.00 1.40
1389 1438 7.587757 GCAAATATTAGTCTGTGCCGAAAATAG 59.412 37.037 0.00 0.00 0.00 1.73
1415 1479 4.079253 GGGTTTCTTAGATGAGCAAACCA 58.921 43.478 11.78 0.00 45.32 3.67
1416 1480 4.156739 GGGTTTCTTAGATGAGCAAACCAG 59.843 45.833 11.78 0.00 45.32 4.00
1417 1481 4.762251 GGTTTCTTAGATGAGCAAACCAGT 59.238 41.667 6.43 0.00 43.71 4.00
1418 1482 5.241728 GGTTTCTTAGATGAGCAAACCAGTT 59.758 40.000 6.43 0.00 43.71 3.16
1419 1483 6.430000 GGTTTCTTAGATGAGCAAACCAGTTA 59.570 38.462 6.43 0.00 43.71 2.24
1420 1484 7.121315 GGTTTCTTAGATGAGCAAACCAGTTAT 59.879 37.037 6.43 0.00 43.71 1.89
1421 1485 8.515414 GTTTCTTAGATGAGCAAACCAGTTATT 58.485 33.333 0.00 0.00 0.00 1.40
1422 1486 8.635765 TTCTTAGATGAGCAAACCAGTTATTT 57.364 30.769 0.00 0.00 0.00 1.40
1423 1487 8.635765 TCTTAGATGAGCAAACCAGTTATTTT 57.364 30.769 0.00 0.00 0.00 1.82
1424 1488 8.730680 TCTTAGATGAGCAAACCAGTTATTTTC 58.269 33.333 0.00 0.00 0.00 2.29
1425 1489 8.635765 TTAGATGAGCAAACCAGTTATTTTCT 57.364 30.769 0.00 0.00 0.00 2.52
1426 1490 9.733556 TTAGATGAGCAAACCAGTTATTTTCTA 57.266 29.630 0.00 0.00 0.00 2.10
1427 1491 8.045176 AGATGAGCAAACCAGTTATTTTCTAC 57.955 34.615 0.00 0.00 0.00 2.59
1428 1492 6.569179 TGAGCAAACCAGTTATTTTCTACC 57.431 37.500 0.00 0.00 0.00 3.18
1429 1493 6.303839 TGAGCAAACCAGTTATTTTCTACCT 58.696 36.000 0.00 0.00 0.00 3.08
1430 1494 6.775629 TGAGCAAACCAGTTATTTTCTACCTT 59.224 34.615 0.00 0.00 0.00 3.50
1431 1495 7.286775 TGAGCAAACCAGTTATTTTCTACCTTT 59.713 33.333 0.00 0.00 0.00 3.11
1432 1496 8.018537 AGCAAACCAGTTATTTTCTACCTTTT 57.981 30.769 0.00 0.00 0.00 2.27
1433 1497 8.482943 AGCAAACCAGTTATTTTCTACCTTTTT 58.517 29.630 0.00 0.00 0.00 1.94
1434 1498 8.547894 GCAAACCAGTTATTTTCTACCTTTTTG 58.452 33.333 0.00 0.00 0.00 2.44
1435 1499 9.594478 CAAACCAGTTATTTTCTACCTTTTTGT 57.406 29.630 0.00 0.00 0.00 2.83
1438 1502 9.811995 ACCAGTTATTTTCTACCTTTTTGTTTC 57.188 29.630 0.00 0.00 0.00 2.78
1439 1503 9.810545 CCAGTTATTTTCTACCTTTTTGTTTCA 57.189 29.630 0.00 0.00 0.00 2.69
1445 1509 8.527567 TTTTCTACCTTTTTGTTTCAACAGTG 57.472 30.769 0.00 0.00 40.50 3.66
1559 1713 7.554118 CCTTGTAATATGGTCTTTCTGTGATGT 59.446 37.037 0.00 0.00 0.00 3.06
1577 1731 3.165058 TGTGATCGCAGGAATACTCAC 57.835 47.619 4.45 0.00 31.91 3.51
1716 1870 4.402793 GCTACATTCTTCCTCACTAGACCA 59.597 45.833 0.00 0.00 0.00 4.02
1819 1976 4.639310 TGCATTGTTGACCTGCAAAATTTT 59.361 33.333 0.00 0.00 42.53 1.82
1820 1977 5.207033 GCATTGTTGACCTGCAAAATTTTC 58.793 37.500 0.00 0.00 38.44 2.29
1821 1978 5.007921 GCATTGTTGACCTGCAAAATTTTCT 59.992 36.000 0.00 0.00 38.44 2.52
1822 1979 6.202570 GCATTGTTGACCTGCAAAATTTTCTA 59.797 34.615 0.00 0.00 38.44 2.10
1823 1980 7.569957 GCATTGTTGACCTGCAAAATTTTCTAG 60.570 37.037 0.00 2.50 38.44 2.43
1824 1981 5.841810 TGTTGACCTGCAAAATTTTCTAGG 58.158 37.500 20.65 20.65 38.44 3.02
1825 1982 5.221422 TGTTGACCTGCAAAATTTTCTAGGG 60.221 40.000 23.78 15.86 38.44 3.53
1826 1983 3.831911 TGACCTGCAAAATTTTCTAGGGG 59.168 43.478 23.78 14.60 0.00 4.79
1827 1984 4.086457 GACCTGCAAAATTTTCTAGGGGA 58.914 43.478 23.78 6.96 0.00 4.81
1828 1985 3.832490 ACCTGCAAAATTTTCTAGGGGAC 59.168 43.478 23.78 4.22 0.00 4.46
1829 1986 3.831911 CCTGCAAAATTTTCTAGGGGACA 59.168 43.478 16.90 3.07 0.00 4.02
1830 1987 4.467438 CCTGCAAAATTTTCTAGGGGACAT 59.533 41.667 16.90 0.00 0.00 3.06
1831 1988 5.656416 CCTGCAAAATTTTCTAGGGGACATA 59.344 40.000 16.90 0.00 0.00 2.29
1832 1989 6.183360 CCTGCAAAATTTTCTAGGGGACATAG 60.183 42.308 16.90 0.00 0.00 2.23
1833 1990 6.252995 TGCAAAATTTTCTAGGGGACATAGT 58.747 36.000 0.00 0.00 0.00 2.12
1834 1991 7.406916 TGCAAAATTTTCTAGGGGACATAGTA 58.593 34.615 0.00 0.00 0.00 1.82
1835 1992 7.338449 TGCAAAATTTTCTAGGGGACATAGTAC 59.662 37.037 0.00 0.00 0.00 2.73
1836 1993 7.556635 GCAAAATTTTCTAGGGGACATAGTACT 59.443 37.037 0.00 0.00 0.00 2.73
1837 1994 9.462606 CAAAATTTTCTAGGGGACATAGTACTT 57.537 33.333 0.00 0.00 0.00 2.24
1840 1997 9.503369 AATTTTCTAGGGGACATAGTACTTAGT 57.497 33.333 0.00 0.00 0.00 2.24
1842 1999 8.986929 TTTCTAGGGGACATAGTACTTAGTAC 57.013 38.462 14.13 14.13 39.10 2.73
1843 2000 7.696618 TCTAGGGGACATAGTACTTAGTACA 57.303 40.000 22.48 10.38 41.03 2.90
1844 2001 7.512992 TCTAGGGGACATAGTACTTAGTACAC 58.487 42.308 22.48 1.85 41.03 2.90
1845 2002 6.083487 AGGGGACATAGTACTTAGTACACA 57.917 41.667 22.48 11.40 41.03 3.72
1846 2003 5.890419 AGGGGACATAGTACTTAGTACACAC 59.110 44.000 22.48 10.17 41.03 3.82
1847 2004 5.653769 GGGGACATAGTACTTAGTACACACA 59.346 44.000 22.48 6.90 41.03 3.72
1848 2005 6.323225 GGGGACATAGTACTTAGTACACACAT 59.677 42.308 22.48 8.67 41.03 3.21
1849 2006 7.503566 GGGGACATAGTACTTAGTACACACATA 59.496 40.741 22.48 7.87 41.03 2.29
1850 2007 8.348507 GGGACATAGTACTTAGTACACACATAC 58.651 40.741 22.48 8.39 41.03 2.39
1851 2008 8.896744 GGACATAGTACTTAGTACACACATACA 58.103 37.037 22.48 0.41 41.03 2.29
1897 2054 1.340405 ACAGCCATGCTTCAACTAGGG 60.340 52.381 0.00 0.00 36.40 3.53
1904 2061 0.179097 GCTTCAACTAGGGGAGCTCG 60.179 60.000 7.83 0.00 0.00 5.03
1907 2064 0.614979 TCAACTAGGGGAGCTCGCTT 60.615 55.000 27.60 23.52 39.51 4.68
1944 2101 0.602638 CAGTACACTGCAAAGCCCGA 60.603 55.000 0.00 0.00 37.15 5.14
1945 2102 0.324943 AGTACACTGCAAAGCCCGAT 59.675 50.000 0.00 0.00 0.00 4.18
1958 2115 1.635663 GCCCGATCGTCAAGTTGGTG 61.636 60.000 15.09 0.00 0.00 4.17
1987 2144 1.257743 CTGGGAAGTTCTCGTCCAGA 58.742 55.000 16.72 0.00 42.56 3.86
1990 2147 0.109226 GGAAGTTCTCGTCCAGACCG 60.109 60.000 2.25 0.00 40.91 4.79
1991 2148 0.733223 GAAGTTCTCGTCCAGACCGC 60.733 60.000 0.00 0.00 0.00 5.68
1993 2150 2.981909 TTCTCGTCCAGACCGCGT 60.982 61.111 4.92 0.00 0.00 6.01
1994 2151 3.263503 TTCTCGTCCAGACCGCGTG 62.264 63.158 4.92 0.00 0.00 5.34
1995 2152 4.778415 CTCGTCCAGACCGCGTGG 62.778 72.222 14.93 14.93 42.84 4.94
2014 2171 5.212194 CGTGGTTGGATAAAAGAAACTGTG 58.788 41.667 0.00 0.00 0.00 3.66
2030 2187 4.178956 ACTGTGTTATGGTTGGGACTTT 57.821 40.909 0.00 0.00 0.00 2.66
2059 2216 8.134202 TGTCTATGGTTTTTCTCACATCTCTA 57.866 34.615 0.00 0.00 0.00 2.43
2148 2306 1.882912 TGCACACATCTCCTGTTGTC 58.117 50.000 0.00 0.00 35.29 3.18
2187 2345 4.688413 GTCTTCCTGACTGAAGCTTTACAG 59.312 45.833 12.38 12.38 41.23 2.74
2205 2363 7.921745 GCTTTACAGTCTATTGGAAGTACCTAG 59.078 40.741 0.00 0.00 39.86 3.02
2206 2364 5.855740 ACAGTCTATTGGAAGTACCTAGC 57.144 43.478 0.00 0.00 39.86 3.42
2209 2367 5.594725 CAGTCTATTGGAAGTACCTAGCTCA 59.405 44.000 0.00 0.00 39.86 4.26
2347 2508 7.362056 CCATTGTCAGAAGAAATCATTTACCGT 60.362 37.037 0.00 0.00 0.00 4.83
2395 2556 0.301687 CGATGAAATGGAGGAACGCG 59.698 55.000 3.53 3.53 0.00 6.01
2442 2603 0.614979 GTAGCACACCTCTCAGGGGA 60.615 60.000 0.00 0.00 43.10 4.81
2479 2640 2.568031 CGTCGTCGGATGCATCACG 61.568 63.158 27.25 26.30 0.00 4.35
2493 2654 3.134985 TGCATCACGGGGTTAGCTTATTA 59.865 43.478 0.00 0.00 0.00 0.98
2533 2694 4.012374 CTGCTTCATTTACCATCCACAGT 58.988 43.478 0.00 0.00 0.00 3.55
2547 2708 1.665735 CCACAGTTTGTACAATGCGGC 60.666 52.381 9.56 0.00 0.00 6.53
2557 2718 2.755836 ACAATGCGGCGATATTGTTC 57.244 45.000 26.41 3.96 43.00 3.18
2563 2724 2.198406 GCGGCGATATTGTTCACTACA 58.802 47.619 12.98 0.00 34.12 2.74
2601 2762 5.491078 TGTGTTTTAGGGGATAGTCAGGAAT 59.509 40.000 0.00 0.00 0.00 3.01
2629 2790 7.011950 TGGATACAGTTCATTAATACTTTGGCG 59.988 37.037 0.00 0.00 46.17 5.69
2737 2902 6.210784 CGGTTGATCCCCACTATTTCTATCTA 59.789 42.308 0.00 0.00 0.00 1.98
2747 2912 7.716998 CCCACTATTTCTATCTAAACATGCACT 59.283 37.037 0.00 0.00 0.00 4.40
2759 2924 2.079158 ACATGCACTCATTTCACCTCG 58.921 47.619 0.00 0.00 0.00 4.63
2785 2950 2.091640 ATGCCACACCATCAACCCCA 62.092 55.000 0.00 0.00 0.00 4.96
2791 2956 4.541705 CCACACCATCAACCCCATTAATA 58.458 43.478 0.00 0.00 0.00 0.98
2815 2980 3.438216 TTTCTCTCAATGTGCATGGGA 57.562 42.857 0.00 0.00 0.00 4.37
2816 2981 3.438216 TTCTCTCAATGTGCATGGGAA 57.562 42.857 0.00 0.00 0.00 3.97
2817 2982 3.438216 TCTCTCAATGTGCATGGGAAA 57.562 42.857 0.00 0.00 0.00 3.13
2818 2983 3.972133 TCTCTCAATGTGCATGGGAAAT 58.028 40.909 0.00 0.00 0.00 2.17
2819 2984 4.346730 TCTCTCAATGTGCATGGGAAATT 58.653 39.130 0.00 0.00 0.00 1.82
2820 2985 4.400251 TCTCTCAATGTGCATGGGAAATTC 59.600 41.667 0.00 0.00 0.00 2.17
2821 2986 4.346730 TCTCAATGTGCATGGGAAATTCT 58.653 39.130 0.00 0.00 0.00 2.40
2822 2987 5.508567 TCTCAATGTGCATGGGAAATTCTA 58.491 37.500 0.00 0.00 0.00 2.10
2823 2988 5.357878 TCTCAATGTGCATGGGAAATTCTAC 59.642 40.000 0.00 0.00 0.00 2.59
2824 2989 5.263599 TCAATGTGCATGGGAAATTCTACT 58.736 37.500 0.00 0.00 0.00 2.57
2825 2990 5.716228 TCAATGTGCATGGGAAATTCTACTT 59.284 36.000 0.00 0.00 0.00 2.24
2826 2991 6.889177 TCAATGTGCATGGGAAATTCTACTTA 59.111 34.615 0.00 0.00 0.00 2.24
2827 2992 7.560991 TCAATGTGCATGGGAAATTCTACTTAT 59.439 33.333 0.00 0.00 0.00 1.73
2828 2993 8.849168 CAATGTGCATGGGAAATTCTACTTATA 58.151 33.333 0.00 0.00 0.00 0.98
2829 2994 8.627208 ATGTGCATGGGAAATTCTACTTATAG 57.373 34.615 0.00 0.00 0.00 1.31
2830 2995 6.486657 TGTGCATGGGAAATTCTACTTATAGC 59.513 38.462 0.00 0.00 0.00 2.97
2831 2996 6.486657 GTGCATGGGAAATTCTACTTATAGCA 59.513 38.462 0.00 0.00 0.00 3.49
2832 2997 7.175641 GTGCATGGGAAATTCTACTTATAGCAT 59.824 37.037 0.00 0.00 0.00 3.79
2869 3034 2.975193 CACATTGCACTTCATCAACACG 59.025 45.455 0.00 0.00 0.00 4.49
2913 3078 2.403037 GCGACGAACACACTACTTGTAC 59.597 50.000 0.00 0.00 35.67 2.90
2927 3092 6.090898 CACTACTTGTACTTCACTTGGTATGC 59.909 42.308 0.00 0.00 0.00 3.14
3013 3178 9.630098 GACAATACTTCAATGTTTGATTCACAT 57.370 29.630 0.00 0.00 39.84 3.21
3057 3222 0.397941 CTCCACCTCACCACACATGT 59.602 55.000 0.00 0.00 0.00 3.21
3112 3333 8.701895 AGTAATTGAATCAAAGCATGGATGAAT 58.298 29.630 0.00 0.00 0.00 2.57
3198 3419 3.354233 AGGTTTTTATTGGGGTTGGGT 57.646 42.857 0.00 0.00 0.00 4.51
3201 3422 3.244284 GGTTTTTATTGGGGTTGGGTGTC 60.244 47.826 0.00 0.00 0.00 3.67
3221 3442 7.398047 GGGTGTCTTTATTATGGTTTAGGGTTT 59.602 37.037 0.00 0.00 0.00 3.27
3244 3465 5.955488 TCTAACCAAGAGAAGACGATGAAG 58.045 41.667 0.00 0.00 0.00 3.02
3260 3481 4.572389 CGATGAAGAAGAAATCAATCGGGT 59.428 41.667 0.00 0.00 35.88 5.28
3302 3523 5.245531 TGTTTGTCAGATAGGCTTACTTGG 58.754 41.667 0.00 0.00 0.00 3.61
3329 3552 4.058124 GCGTGGCTACATCATAGATGAAA 58.942 43.478 13.46 1.32 40.69 2.69
3344 3567 9.559732 TCATAGATGAAAGAAACACAAAGAAGA 57.440 29.630 0.00 0.00 33.08 2.87
3371 3594 3.634397 TGATAGTGGAGAAAAGGGCAG 57.366 47.619 0.00 0.00 0.00 4.85
3379 3602 3.701040 TGGAGAAAAGGGCAGCAATAATC 59.299 43.478 0.00 0.00 0.00 1.75
3395 3618 2.865119 AATCACATGCACTCACCTCA 57.135 45.000 0.00 0.00 0.00 3.86
3402 3625 0.250467 TGCACTCACCTCAAGGAAGC 60.250 55.000 2.30 0.28 38.94 3.86
3405 3629 1.345741 CACTCACCTCAAGGAAGCTGA 59.654 52.381 2.30 0.00 38.94 4.26
3417 3641 1.339055 GGAAGCTGAGGTGCACATACA 60.339 52.381 20.43 13.62 34.99 2.29
3419 3643 0.686789 AGCTGAGGTGCACATACACA 59.313 50.000 20.43 5.12 42.55 3.72
3426 3650 1.679944 GGTGCACATACACATCTGGCT 60.680 52.381 20.43 0.00 42.55 4.75
3427 3651 1.667724 GTGCACATACACATCTGGCTC 59.332 52.381 13.17 0.00 40.40 4.70
3453 3677 9.326413 CGGTTCATCATTAATTACCTAAACTCT 57.674 33.333 0.00 0.00 0.00 3.24
3459 3683 7.280356 TCATTAATTACCTAAACTCTCTGGGC 58.720 38.462 0.00 0.00 0.00 5.36
3460 3684 4.505324 AATTACCTAAACTCTCTGGGCC 57.495 45.455 0.00 0.00 0.00 5.80
3461 3685 2.634639 TACCTAAACTCTCTGGGCCA 57.365 50.000 5.85 5.85 0.00 5.36
3462 3686 1.742308 ACCTAAACTCTCTGGGCCAA 58.258 50.000 8.04 0.00 0.00 4.52
3463 3687 2.279173 ACCTAAACTCTCTGGGCCAAT 58.721 47.619 8.04 0.00 0.00 3.16
3464 3688 3.460825 ACCTAAACTCTCTGGGCCAATA 58.539 45.455 8.04 0.00 0.00 1.90
3465 3689 3.456277 ACCTAAACTCTCTGGGCCAATAG 59.544 47.826 8.04 8.55 0.00 1.73
3466 3690 2.426842 AAACTCTCTGGGCCAATAGC 57.573 50.000 8.04 0.00 42.60 2.97
3467 3691 1.589414 AACTCTCTGGGCCAATAGCT 58.411 50.000 8.04 0.00 43.05 3.32
3468 3692 1.127343 ACTCTCTGGGCCAATAGCTC 58.873 55.000 8.04 0.00 45.08 4.09
3469 3693 0.396060 CTCTCTGGGCCAATAGCTCC 59.604 60.000 8.04 0.00 43.71 4.70
3470 3694 0.030705 TCTCTGGGCCAATAGCTCCT 60.031 55.000 8.04 0.00 43.71 3.69
3471 3695 0.108207 CTCTGGGCCAATAGCTCCTG 59.892 60.000 8.04 0.00 43.71 3.86
3472 3696 0.621571 TCTGGGCCAATAGCTCCTGT 60.622 55.000 8.04 0.00 43.71 4.00
3473 3697 0.465097 CTGGGCCAATAGCTCCTGTG 60.465 60.000 8.04 0.00 43.71 3.66
3474 3698 1.825622 GGGCCAATAGCTCCTGTGC 60.826 63.158 4.39 0.00 43.05 4.57
3475 3699 2.182842 GGCCAATAGCTCCTGTGCG 61.183 63.158 0.00 0.00 43.05 5.34
3476 3700 1.153369 GCCAATAGCTCCTGTGCGA 60.153 57.895 0.00 0.00 38.99 5.10
3477 3701 1.432270 GCCAATAGCTCCTGTGCGAC 61.432 60.000 0.00 0.00 38.99 5.19
3478 3702 1.148157 CCAATAGCTCCTGTGCGACG 61.148 60.000 0.00 0.00 38.13 5.12
3479 3703 0.458543 CAATAGCTCCTGTGCGACGT 60.459 55.000 0.00 0.00 38.13 4.34
3480 3704 0.246635 AATAGCTCCTGTGCGACGTT 59.753 50.000 0.00 0.00 38.13 3.99
3481 3705 0.246635 ATAGCTCCTGTGCGACGTTT 59.753 50.000 0.00 0.00 38.13 3.60
3482 3706 0.032952 TAGCTCCTGTGCGACGTTTT 59.967 50.000 0.00 0.00 38.13 2.43
3483 3707 0.814010 AGCTCCTGTGCGACGTTTTT 60.814 50.000 0.00 0.00 38.13 1.94
3484 3708 0.657368 GCTCCTGTGCGACGTTTTTG 60.657 55.000 0.00 0.00 0.00 2.44
3485 3709 0.934496 CTCCTGTGCGACGTTTTTGA 59.066 50.000 0.00 0.00 0.00 2.69
3486 3710 0.934496 TCCTGTGCGACGTTTTTGAG 59.066 50.000 0.00 0.00 0.00 3.02
3487 3711 0.041312 CCTGTGCGACGTTTTTGAGG 60.041 55.000 0.00 0.00 0.00 3.86
3488 3712 0.655733 CTGTGCGACGTTTTTGAGGT 59.344 50.000 0.00 0.00 0.00 3.85
3489 3713 0.375454 TGTGCGACGTTTTTGAGGTG 59.625 50.000 0.00 0.00 0.00 4.00
3490 3714 0.653636 GTGCGACGTTTTTGAGGTGA 59.346 50.000 0.00 0.00 0.00 4.02
3491 3715 1.062880 GTGCGACGTTTTTGAGGTGAA 59.937 47.619 0.00 0.00 0.00 3.18
3492 3716 1.944024 TGCGACGTTTTTGAGGTGAAT 59.056 42.857 0.00 0.00 0.00 2.57
3493 3717 2.356382 TGCGACGTTTTTGAGGTGAATT 59.644 40.909 0.00 0.00 0.00 2.17
3494 3718 2.719046 GCGACGTTTTTGAGGTGAATTG 59.281 45.455 0.00 0.00 0.00 2.32
3495 3719 3.296628 CGACGTTTTTGAGGTGAATTGG 58.703 45.455 0.00 0.00 0.00 3.16
3496 3720 3.049912 GACGTTTTTGAGGTGAATTGGC 58.950 45.455 0.00 0.00 0.00 4.52
3497 3721 2.428890 ACGTTTTTGAGGTGAATTGGCA 59.571 40.909 0.00 0.00 0.00 4.92
3498 3722 3.118956 ACGTTTTTGAGGTGAATTGGCAA 60.119 39.130 0.68 0.68 0.00 4.52
3499 3723 3.490526 CGTTTTTGAGGTGAATTGGCAAG 59.509 43.478 5.96 0.00 0.00 4.01
3500 3724 4.692228 GTTTTTGAGGTGAATTGGCAAGA 58.308 39.130 5.96 0.00 0.00 3.02
3501 3725 4.589216 TTTTGAGGTGAATTGGCAAGAG 57.411 40.909 5.96 0.00 0.00 2.85
3502 3726 2.957402 TGAGGTGAATTGGCAAGAGT 57.043 45.000 5.96 0.00 0.00 3.24
3503 3727 2.507484 TGAGGTGAATTGGCAAGAGTG 58.493 47.619 5.96 0.00 0.00 3.51
3512 3736 3.319904 GCAAGAGTGCGACGTTGT 58.680 55.556 4.37 0.00 41.93 3.32
3513 3737 1.641677 GCAAGAGTGCGACGTTGTT 59.358 52.632 4.37 0.00 41.93 2.83
3514 3738 0.383124 GCAAGAGTGCGACGTTGTTC 60.383 55.000 4.37 0.68 41.93 3.18
3515 3739 0.111704 CAAGAGTGCGACGTTGTTCG 60.112 55.000 4.37 0.00 46.00 3.95
3516 3740 0.248743 AAGAGTGCGACGTTGTTCGA 60.249 50.000 4.37 0.00 41.78 3.71
3517 3741 0.660595 AGAGTGCGACGTTGTTCGAG 60.661 55.000 4.37 0.00 41.78 4.04
3518 3742 2.167918 GTGCGACGTTGTTCGAGC 59.832 61.111 4.37 0.00 41.78 5.03
3519 3743 3.391631 TGCGACGTTGTTCGAGCG 61.392 61.111 4.37 0.00 44.15 5.03
3520 3744 3.095278 GCGACGTTGTTCGAGCGA 61.095 61.111 4.37 0.00 41.78 4.93
3521 3745 2.641783 GCGACGTTGTTCGAGCGAA 61.642 57.895 4.37 0.55 41.78 4.70
3522 3746 1.941476 GCGACGTTGTTCGAGCGAAT 61.941 55.000 8.66 0.00 41.78 3.34
3523 3747 0.246374 CGACGTTGTTCGAGCGAATG 60.246 55.000 8.66 2.77 41.78 2.67
3524 3748 0.093026 GACGTTGTTCGAGCGAATGG 59.907 55.000 8.66 1.96 42.86 3.16
3525 3749 1.225745 CGTTGTTCGAGCGAATGGC 60.226 57.895 8.66 0.00 42.86 4.40
3534 3758 4.465512 GCGAATGGCTGTGGTGCG 62.466 66.667 0.00 0.00 39.11 5.34
3535 3759 2.741985 CGAATGGCTGTGGTGCGA 60.742 61.111 0.00 0.00 0.00 5.10
3536 3760 2.870372 GAATGGCTGTGGTGCGAC 59.130 61.111 0.00 0.00 0.00 5.19
3537 3761 1.965930 GAATGGCTGTGGTGCGACA 60.966 57.895 0.00 0.00 0.00 4.35
3538 3762 2.187599 GAATGGCTGTGGTGCGACAC 62.188 60.000 3.83 3.83 41.68 3.67
3544 3768 3.086733 TGTGGTGCGACACATTTGA 57.913 47.368 8.96 0.00 45.70 2.69
3545 3769 0.943673 TGTGGTGCGACACATTTGAG 59.056 50.000 8.96 0.00 45.70 3.02
3546 3770 0.385974 GTGGTGCGACACATTTGAGC 60.386 55.000 11.20 0.00 40.99 4.26
3547 3771 1.154413 GGTGCGACACATTTGAGCG 60.154 57.895 11.20 0.00 35.86 5.03
3548 3772 1.569493 GTGCGACACATTTGAGCGT 59.431 52.632 5.30 0.00 34.08 5.07
3549 3773 0.722469 GTGCGACACATTTGAGCGTG 60.722 55.000 5.30 0.00 39.10 5.34
3551 3775 0.787787 GCGACACATTTGAGCGTGTA 59.212 50.000 0.00 0.00 46.06 2.90
3552 3776 1.193650 GCGACACATTTGAGCGTGTAA 59.806 47.619 0.00 0.00 46.06 2.41
3553 3777 2.349060 GCGACACATTTGAGCGTGTAAA 60.349 45.455 0.00 0.00 46.06 2.01
3554 3778 3.666902 GCGACACATTTGAGCGTGTAAAT 60.667 43.478 0.00 0.00 46.06 1.40
3555 3779 4.434989 GCGACACATTTGAGCGTGTAAATA 60.435 41.667 0.00 0.00 46.06 1.40
3556 3780 5.248087 CGACACATTTGAGCGTGTAAATAG 58.752 41.667 0.00 0.00 46.06 1.73
3557 3781 4.969816 ACACATTTGAGCGTGTAAATAGC 58.030 39.130 0.00 0.00 44.32 2.97
3558 3782 4.142687 ACACATTTGAGCGTGTAAATAGCC 60.143 41.667 0.00 0.00 44.32 3.93
3559 3783 3.377172 ACATTTGAGCGTGTAAATAGCCC 59.623 43.478 0.00 0.00 0.00 5.19
3560 3784 2.772077 TTGAGCGTGTAAATAGCCCA 57.228 45.000 0.00 0.00 0.00 5.36
3561 3785 2.309528 TGAGCGTGTAAATAGCCCAG 57.690 50.000 0.00 0.00 0.00 4.45
3562 3786 1.134521 TGAGCGTGTAAATAGCCCAGG 60.135 52.381 0.00 0.00 0.00 4.45
3563 3787 0.180406 AGCGTGTAAATAGCCCAGGG 59.820 55.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.682936 AATTGTCATCAAGTTAAGAGTGTTCT 57.317 30.769 0.00 0.00 36.97 3.01
1 2 8.017946 GGAATTGTCATCAAGTTAAGAGTGTTC 58.982 37.037 0.00 0.00 36.97 3.18
2 3 7.721399 AGGAATTGTCATCAAGTTAAGAGTGTT 59.279 33.333 0.00 0.00 36.97 3.32
3 4 7.227156 AGGAATTGTCATCAAGTTAAGAGTGT 58.773 34.615 0.00 0.00 36.97 3.55
32 33 7.417612 GCATATCACGTGTTTCAATAATCCTT 58.582 34.615 16.51 0.00 0.00 3.36
42 43 3.438781 TCCAAAGGCATATCACGTGTTTC 59.561 43.478 16.51 1.76 0.00 2.78
49 50 7.636150 AATGCTATATCCAAAGGCATATCAC 57.364 36.000 0.00 0.00 41.85 3.06
56 57 7.709149 AGGAATTAATGCTATATCCAAAGGC 57.291 36.000 4.78 0.00 0.00 4.35
85 91 8.970859 AAGACATTTTCCCTATCAATCTGTAG 57.029 34.615 0.00 0.00 0.00 2.74
105 111 1.250328 CATTGGCTTGCCAGAAGACA 58.750 50.000 14.33 0.00 32.50 3.41
106 112 0.108945 GCATTGGCTTGCCAGAAGAC 60.109 55.000 14.33 0.00 36.60 3.01
143 149 0.836400 AGACCGGTTCTGTGGACCAT 60.836 55.000 9.42 0.00 31.12 3.55
148 154 1.254026 TCTGTAGACCGGTTCTGTGG 58.746 55.000 9.42 0.00 35.55 4.17
156 162 0.824109 TCTTGGCATCTGTAGACCGG 59.176 55.000 0.00 0.00 0.00 5.28
158 164 3.895232 TCTTCTTGGCATCTGTAGACC 57.105 47.619 0.00 0.00 0.00 3.85
166 172 3.949132 ACCTCTTCTTCTTCTTGGCATC 58.051 45.455 0.00 0.00 0.00 3.91
183 189 1.672145 GCGGAACTTCCTGTGTACCTC 60.672 57.143 6.25 0.00 33.30 3.85
201 207 2.960512 TTGTTGAATGCCCGTCGCG 61.961 57.895 0.00 0.00 42.08 5.87
205 211 0.030101 CAACGTTGTTGAATGCCCGT 59.970 50.000 20.21 0.00 0.00 5.28
222 228 3.410631 TCGTCCAGCTTTGTATTCCAA 57.589 42.857 0.00 0.00 0.00 3.53
224 230 2.418976 GGTTCGTCCAGCTTTGTATTCC 59.581 50.000 0.00 0.00 35.97 3.01
279 285 1.179814 GGTACAGGGCGATCTCCGAT 61.180 60.000 0.00 0.00 41.76 4.18
345 351 3.117398 CCAGGAAATGAGGGATGATGGAA 60.117 47.826 0.00 0.00 0.00 3.53
366 372 4.778143 AGCCGGCCAATGTCGTCC 62.778 66.667 26.15 0.00 38.09 4.79
416 422 2.124942 GCAGGGGCGAAAGAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
486 492 1.134521 TCAACCAAGACACGCTCAAGT 60.135 47.619 0.00 0.00 0.00 3.16
499 505 4.881273 CGGGACATCATAAATCTCAACCAA 59.119 41.667 0.00 0.00 0.00 3.67
615 621 2.015456 TCCGGCACAGGATGATATCT 57.985 50.000 3.98 0.00 39.69 1.98
619 625 0.620556 ACTTTCCGGCACAGGATGAT 59.379 50.000 0.00 0.00 40.48 2.45
681 687 1.379044 CCCTCACTCCACATTGGGC 60.379 63.158 0.00 0.00 38.32 5.36
685 691 0.693049 GACACCCCTCACTCCACATT 59.307 55.000 0.00 0.00 0.00 2.71
694 700 4.271807 AGATGATTCTAGACACCCCTCA 57.728 45.455 0.00 0.00 0.00 3.86
700 706 7.201478 GCAACAACAGTAGATGATTCTAGACAC 60.201 40.741 0.00 0.00 35.12 3.67
750 761 4.566004 TGTTCTCTTCACCGGTCTTATTG 58.434 43.478 2.59 0.00 0.00 1.90
801 812 9.944376 ATGATTAATAAGAGCATACATAACGGT 57.056 29.630 0.00 0.00 0.00 4.83
887 898 2.354103 CCGAGATTGACACAGGACACAT 60.354 50.000 0.00 0.00 0.00 3.21
894 905 1.078759 GACGCCCGAGATTGACACAG 61.079 60.000 0.00 0.00 0.00 3.66
895 906 1.080093 GACGCCCGAGATTGACACA 60.080 57.895 0.00 0.00 0.00 3.72
896 907 1.810030 GGACGCCCGAGATTGACAC 60.810 63.158 0.00 0.00 0.00 3.67
1049 1061 0.108281 GGTTCTACTTCTCACGGGGC 60.108 60.000 0.00 0.00 0.00 5.80
1313 1338 7.281549 AGCAAAGCAATTTTCAAGAGTGAATTT 59.718 29.630 0.00 0.00 43.29 1.82
1319 1344 5.910614 AGAAGCAAAGCAATTTTCAAGAGT 58.089 33.333 0.00 0.00 0.00 3.24
1329 1354 2.366266 TCAGCCAAAGAAGCAAAGCAAT 59.634 40.909 0.00 0.00 0.00 3.56
1352 1377 2.473530 AATATTTGCGCACCATGTCG 57.526 45.000 11.12 0.00 0.00 4.35
1359 1408 3.354397 GCACAGACTAATATTTGCGCAC 58.646 45.455 11.12 0.00 0.00 5.34
1363 1412 4.875544 TTCGGCACAGACTAATATTTGC 57.124 40.909 0.00 0.00 0.00 3.68
1395 1459 5.948992 ACTGGTTTGCTCATCTAAGAAAC 57.051 39.130 0.00 0.00 0.00 2.78
1402 1466 7.121315 GGTAGAAAATAACTGGTTTGCTCATCT 59.879 37.037 0.00 0.00 0.00 2.90
1419 1483 9.150348 CACTGTTGAAACAAAAAGGTAGAAAAT 57.850 29.630 0.00 0.00 38.66 1.82
1420 1484 8.361139 TCACTGTTGAAACAAAAAGGTAGAAAA 58.639 29.630 0.00 0.00 38.66 2.29
1421 1485 7.887381 TCACTGTTGAAACAAAAAGGTAGAAA 58.113 30.769 0.00 0.00 38.66 2.52
1422 1486 7.175990 ACTCACTGTTGAAACAAAAAGGTAGAA 59.824 33.333 0.00 0.00 38.66 2.10
1423 1487 6.657541 ACTCACTGTTGAAACAAAAAGGTAGA 59.342 34.615 0.00 0.00 38.66 2.59
1424 1488 6.852664 ACTCACTGTTGAAACAAAAAGGTAG 58.147 36.000 0.00 0.00 38.66 3.18
1425 1489 6.827586 ACTCACTGTTGAAACAAAAAGGTA 57.172 33.333 0.00 0.00 38.66 3.08
1426 1490 5.722021 ACTCACTGTTGAAACAAAAAGGT 57.278 34.783 0.00 0.00 38.66 3.50
1427 1491 8.702163 AATAACTCACTGTTGAAACAAAAAGG 57.298 30.769 0.00 0.00 39.55 3.11
1430 1494 9.482627 ACAAAATAACTCACTGTTGAAACAAAA 57.517 25.926 0.00 0.00 39.55 2.44
1432 1496 9.562583 GTACAAAATAACTCACTGTTGAAACAA 57.437 29.630 0.00 0.00 39.55 2.83
1433 1497 8.952278 AGTACAAAATAACTCACTGTTGAAACA 58.048 29.630 0.00 0.00 39.55 2.83
1517 1671 4.419522 ACAAGGAATGTGTTTATGACGC 57.580 40.909 0.00 0.00 41.93 5.19
1559 1713 3.701542 AGAAGTGAGTATTCCTGCGATCA 59.298 43.478 0.00 0.00 0.00 2.92
1577 1731 6.054295 CCCATGGAGTATCTGAAGAAAGAAG 58.946 44.000 15.22 0.00 33.73 2.85
1606 1760 4.686944 GCAAATGTCCTCCATACATCCTCA 60.687 45.833 0.00 0.00 36.56 3.86
1716 1870 6.412214 AAGTTACCACTTACTGTTGTCAGTT 58.588 36.000 6.20 0.00 42.53 3.16
1819 1976 7.127801 TGTGTACTAAGTACTATGTCCCCTAGA 59.872 40.741 0.00 0.00 39.49 2.43
1820 1977 7.228308 GTGTGTACTAAGTACTATGTCCCCTAG 59.772 44.444 0.00 0.00 39.49 3.02
1821 1978 7.056635 GTGTGTACTAAGTACTATGTCCCCTA 58.943 42.308 0.00 0.00 39.49 3.53
1822 1979 5.890419 GTGTGTACTAAGTACTATGTCCCCT 59.110 44.000 0.00 0.00 39.49 4.79
1823 1980 5.653769 TGTGTGTACTAAGTACTATGTCCCC 59.346 44.000 0.00 0.00 39.49 4.81
1824 1981 6.764308 TGTGTGTACTAAGTACTATGTCCC 57.236 41.667 0.00 0.00 39.49 4.46
1825 1982 8.896744 TGTATGTGTGTACTAAGTACTATGTCC 58.103 37.037 0.00 0.00 39.49 4.02
1830 1987 9.342308 GGGTATGTATGTGTGTACTAAGTACTA 57.658 37.037 0.00 0.00 39.49 1.82
1831 1988 8.057623 AGGGTATGTATGTGTGTACTAAGTACT 58.942 37.037 0.00 0.00 39.49 2.73
1832 1989 8.133627 CAGGGTATGTATGTGTGTACTAAGTAC 58.866 40.741 0.00 0.00 39.24 2.73
1833 1990 7.835682 ACAGGGTATGTATGTGTGTACTAAGTA 59.164 37.037 0.00 0.00 41.60 2.24
1834 1991 6.666546 ACAGGGTATGTATGTGTGTACTAAGT 59.333 38.462 0.00 0.00 41.60 2.24
1835 1992 7.108841 ACAGGGTATGTATGTGTGTACTAAG 57.891 40.000 0.00 0.00 41.60 2.18
1836 1993 6.664384 TGACAGGGTATGTATGTGTGTACTAA 59.336 38.462 0.00 0.00 44.17 2.24
1837 1994 6.189133 TGACAGGGTATGTATGTGTGTACTA 58.811 40.000 0.00 0.00 44.17 1.82
1838 1995 5.020795 TGACAGGGTATGTATGTGTGTACT 58.979 41.667 0.00 0.00 44.17 2.73
1839 1996 5.333299 TGACAGGGTATGTATGTGTGTAC 57.667 43.478 0.00 0.00 44.17 2.90
1840 1997 6.345298 CATTGACAGGGTATGTATGTGTGTA 58.655 40.000 0.00 0.00 44.17 2.90
1841 1998 4.901197 TTGACAGGGTATGTATGTGTGT 57.099 40.909 0.00 0.00 44.17 3.72
1842 1999 4.035558 GCATTGACAGGGTATGTATGTGTG 59.964 45.833 0.00 0.00 44.17 3.82
1843 2000 4.199310 GCATTGACAGGGTATGTATGTGT 58.801 43.478 0.00 0.00 44.17 3.72
1844 2001 4.198530 TGCATTGACAGGGTATGTATGTG 58.801 43.478 0.00 0.00 44.17 3.21
1845 2002 4.454678 CTGCATTGACAGGGTATGTATGT 58.545 43.478 0.00 0.00 44.17 2.29
1870 2027 0.961019 GAAGCATGGCTGTGGAAACA 59.039 50.000 0.00 0.00 39.62 2.83
1897 2054 1.087501 CTAAACCCAAAGCGAGCTCC 58.912 55.000 8.47 0.68 0.00 4.70
1904 2061 2.742774 CAACAGTGCTAAACCCAAAGC 58.257 47.619 0.00 0.00 39.25 3.51
1942 2099 0.670546 AGGCACCAACTTGACGATCG 60.671 55.000 14.88 14.88 0.00 3.69
1944 2101 1.072331 AGAAGGCACCAACTTGACGAT 59.928 47.619 0.00 0.00 0.00 3.73
1945 2102 0.468226 AGAAGGCACCAACTTGACGA 59.532 50.000 0.00 0.00 0.00 4.20
1958 2115 1.270826 GAACTTCCCAGCAAAGAAGGC 59.729 52.381 12.46 3.14 43.10 4.35
1990 2147 4.226761 CAGTTTCTTTTATCCAACCACGC 58.773 43.478 0.00 0.00 0.00 5.34
1991 2148 5.212194 CACAGTTTCTTTTATCCAACCACG 58.788 41.667 0.00 0.00 0.00 4.94
1993 2150 6.783708 AACACAGTTTCTTTTATCCAACCA 57.216 33.333 0.00 0.00 0.00 3.67
1994 2151 7.812669 CCATAACACAGTTTCTTTTATCCAACC 59.187 37.037 0.00 0.00 0.00 3.77
1995 2152 8.357402 ACCATAACACAGTTTCTTTTATCCAAC 58.643 33.333 0.00 0.00 0.00 3.77
1996 2153 8.472007 ACCATAACACAGTTTCTTTTATCCAA 57.528 30.769 0.00 0.00 0.00 3.53
2000 2157 7.507616 TCCCAACCATAACACAGTTTCTTTTAT 59.492 33.333 0.00 0.00 0.00 1.40
2014 2171 5.476945 AGACATCAAAAGTCCCAACCATAAC 59.523 40.000 0.00 0.00 36.68 1.89
2030 2187 7.884877 AGATGTGAGAAAAACCATAGACATCAA 59.115 33.333 0.00 0.00 40.49 2.57
2059 2216 4.586841 GGACCTATCAGTCTGTCAGCTATT 59.413 45.833 0.00 0.00 36.95 1.73
2105 2262 8.647226 GCAATAGTCGAAAAACTGCAATTTAAT 58.353 29.630 0.00 0.00 0.00 1.40
2148 2306 8.341173 GTCAGGAAGACTAATGCAATGAATAAG 58.659 37.037 0.00 0.00 44.09 1.73
2187 2345 6.658188 ATGAGCTAGGTACTTCCAATAGAC 57.342 41.667 0.00 0.00 41.75 2.59
2191 2349 5.957771 TGAATGAGCTAGGTACTTCCAAT 57.042 39.130 11.40 0.00 41.75 3.16
2205 2363 8.700644 GCAATATTTCAGATTGAATGAATGAGC 58.299 33.333 0.00 0.00 36.11 4.26
2206 2364 9.744468 TGCAATATTTCAGATTGAATGAATGAG 57.256 29.630 0.00 0.00 36.11 2.90
2209 2367 8.920174 TCCTGCAATATTTCAGATTGAATGAAT 58.080 29.630 15.61 0.00 36.11 2.57
2270 2431 0.544595 AGCCTAGAGGTTCCACCGTT 60.545 55.000 0.00 0.00 44.90 4.44
2272 2433 1.033574 CTAGCCTAGAGGTTCCACCG 58.966 60.000 0.00 0.00 44.90 4.94
2347 2508 2.062636 AGGGCTGTTAGAAGAAACCCA 58.937 47.619 0.00 0.00 38.39 4.51
2395 2556 4.479619 ACATAACTGAACTTACGACGACC 58.520 43.478 0.00 0.00 0.00 4.79
2437 2598 4.610333 ACAACTGAAAGAAACTTTCCCCT 58.390 39.130 17.64 3.62 37.43 4.79
2442 2603 5.106830 ACGACGAACAACTGAAAGAAACTTT 60.107 36.000 0.00 0.00 37.43 2.66
2479 2640 2.702478 AGTCCGGTAATAAGCTAACCCC 59.298 50.000 0.00 0.00 0.00 4.95
2493 2654 1.228154 GCCAAAGTTCCAGTCCGGT 60.228 57.895 0.00 0.00 35.57 5.28
2533 2694 3.375610 ACAATATCGCCGCATTGTACAAA 59.624 39.130 13.23 0.00 42.17 2.83
2557 2718 7.137490 ACACATTCAAGACATCATTGTAGTG 57.863 36.000 0.00 0.00 35.79 2.74
2563 2724 7.309990 CCCCTAAAACACATTCAAGACATCATT 60.310 37.037 0.00 0.00 0.00 2.57
2601 2762 9.173021 CCAAAGTATTAATGAACTGTATCCACA 57.827 33.333 0.00 0.00 0.00 4.17
2620 2781 2.801679 CGGTAAAAGTGTCGCCAAAGTA 59.198 45.455 0.00 0.00 0.00 2.24
2737 2902 3.058016 CGAGGTGAAATGAGTGCATGTTT 60.058 43.478 0.00 0.00 34.26 2.83
2747 2912 3.205338 CATATGTGGCGAGGTGAAATGA 58.795 45.455 0.00 0.00 0.00 2.57
2791 2956 6.131264 TCCCATGCACATTGAGAGAAATATT 58.869 36.000 0.00 0.00 0.00 1.28
2806 2971 6.486657 TGCTATAAGTAGAATTTCCCATGCAC 59.513 38.462 0.00 0.00 0.00 4.57
2819 2984 9.770097 CATGGAGAAAGAAATGCTATAAGTAGA 57.230 33.333 0.00 0.00 0.00 2.59
2820 2985 9.553064 ACATGGAGAAAGAAATGCTATAAGTAG 57.447 33.333 0.00 0.00 0.00 2.57
2822 2987 9.331282 GTACATGGAGAAAGAAATGCTATAAGT 57.669 33.333 0.00 0.00 0.00 2.24
2823 2988 9.330063 TGTACATGGAGAAAGAAATGCTATAAG 57.670 33.333 0.00 0.00 0.00 1.73
2824 2989 9.109393 GTGTACATGGAGAAAGAAATGCTATAA 57.891 33.333 0.00 0.00 0.00 0.98
2825 2990 8.264347 TGTGTACATGGAGAAAGAAATGCTATA 58.736 33.333 0.00 0.00 0.00 1.31
2826 2991 7.112122 TGTGTACATGGAGAAAGAAATGCTAT 58.888 34.615 0.00 0.00 0.00 2.97
2827 2992 6.472016 TGTGTACATGGAGAAAGAAATGCTA 58.528 36.000 0.00 0.00 0.00 3.49
2828 2993 5.316167 TGTGTACATGGAGAAAGAAATGCT 58.684 37.500 0.00 0.00 0.00 3.79
2829 2994 5.627499 TGTGTACATGGAGAAAGAAATGC 57.373 39.130 0.00 0.00 0.00 3.56
2830 2995 6.529125 GCAATGTGTACATGGAGAAAGAAATG 59.471 38.462 0.00 0.00 36.56 2.32
2831 2996 6.209192 TGCAATGTGTACATGGAGAAAGAAAT 59.791 34.615 0.00 0.00 36.56 2.17
2832 2997 5.534278 TGCAATGTGTACATGGAGAAAGAAA 59.466 36.000 0.00 0.00 36.56 2.52
2841 3006 4.156373 TGATGAAGTGCAATGTGTACATGG 59.844 41.667 0.00 0.00 35.34 3.66
2888 3053 1.856597 AGTAGTGTGTTCGTCGCAAAC 59.143 47.619 0.00 0.00 38.33 2.93
2913 3078 3.064958 CAGCTCATGCATACCAAGTGAAG 59.935 47.826 0.00 0.00 42.74 3.02
2980 3145 9.897744 TCAAACATTGAAGTATTGTCTTTGATC 57.102 29.630 0.00 0.00 36.59 2.92
2987 3152 9.630098 ATGTGAATCAAACATTGAAGTATTGTC 57.370 29.630 0.00 0.00 43.95 3.18
3023 3188 5.247337 TGAGGTGGAGTGTGTACATTATGAA 59.753 40.000 0.00 0.00 0.00 2.57
3028 3193 2.038557 GGTGAGGTGGAGTGTGTACATT 59.961 50.000 0.00 0.00 0.00 2.71
3112 3333 6.049149 GCTTGCTACATTGTCACTCCTATTA 58.951 40.000 0.00 0.00 0.00 0.98
3221 3442 5.710567 TCTTCATCGTCTTCTCTTGGTTAGA 59.289 40.000 0.00 0.00 0.00 2.10
3244 3465 6.693315 TGGATTAACCCGATTGATTTCTTC 57.307 37.500 0.00 0.00 38.00 2.87
3277 3498 6.037610 CCAAGTAAGCCTATCTGACAAACATC 59.962 42.308 0.00 0.00 0.00 3.06
3282 3503 3.873910 GCCAAGTAAGCCTATCTGACAA 58.126 45.455 0.00 0.00 0.00 3.18
3308 3529 5.532557 TCTTTCATCTATGATGTAGCCACG 58.467 41.667 7.33 0.00 36.56 4.94
3344 3567 7.001073 GCCCTTTTCTCCACTATCAATATCTT 58.999 38.462 0.00 0.00 0.00 2.40
3345 3568 6.101734 TGCCCTTTTCTCCACTATCAATATCT 59.898 38.462 0.00 0.00 0.00 1.98
3357 3580 2.897271 TATTGCTGCCCTTTTCTCCA 57.103 45.000 0.00 0.00 0.00 3.86
3371 3594 3.379372 AGGTGAGTGCATGTGATTATTGC 59.621 43.478 0.00 0.00 36.91 3.56
3379 3602 1.162698 CCTTGAGGTGAGTGCATGTG 58.837 55.000 0.00 0.00 0.00 3.21
3395 3618 0.403271 ATGTGCACCTCAGCTTCCTT 59.597 50.000 15.69 0.00 34.99 3.36
3402 3625 2.934553 CAGATGTGTATGTGCACCTCAG 59.065 50.000 15.69 0.00 36.77 3.35
3405 3629 1.679944 GCCAGATGTGTATGTGCACCT 60.680 52.381 15.69 7.20 38.52 4.00
3417 3641 0.904649 TGATGAACCGAGCCAGATGT 59.095 50.000 0.00 0.00 0.00 3.06
3419 3643 4.422073 TTAATGATGAACCGAGCCAGAT 57.578 40.909 0.00 0.00 0.00 2.90
3426 3650 9.321562 GAGTTTAGGTAATTAATGATGAACCGA 57.678 33.333 0.00 0.00 32.43 4.69
3427 3651 9.326413 AGAGTTTAGGTAATTAATGATGAACCG 57.674 33.333 0.00 0.00 32.43 4.44
3453 3677 0.621571 ACAGGAGCTATTGGCCCAGA 60.622 55.000 0.00 0.00 43.05 3.86
3456 3680 1.825622 GCACAGGAGCTATTGGCCC 60.826 63.158 0.00 0.00 43.05 5.80
3459 3683 1.148157 CGTCGCACAGGAGCTATTGG 61.148 60.000 0.00 0.00 0.00 3.16
3460 3684 0.458543 ACGTCGCACAGGAGCTATTG 60.459 55.000 0.00 0.00 0.00 1.90
3461 3685 0.246635 AACGTCGCACAGGAGCTATT 59.753 50.000 0.00 0.00 0.00 1.73
3462 3686 0.246635 AAACGTCGCACAGGAGCTAT 59.753 50.000 0.00 0.00 0.00 2.97
3463 3687 0.032952 AAAACGTCGCACAGGAGCTA 59.967 50.000 0.00 0.00 0.00 3.32
3464 3688 0.814010 AAAAACGTCGCACAGGAGCT 60.814 50.000 0.00 0.00 0.00 4.09
3465 3689 0.657368 CAAAAACGTCGCACAGGAGC 60.657 55.000 0.00 0.00 0.00 4.70
3466 3690 0.934496 TCAAAAACGTCGCACAGGAG 59.066 50.000 0.00 0.00 0.00 3.69
3467 3691 0.934496 CTCAAAAACGTCGCACAGGA 59.066 50.000 0.00 0.00 0.00 3.86
3468 3692 0.041312 CCTCAAAAACGTCGCACAGG 60.041 55.000 0.00 0.00 0.00 4.00
3469 3693 0.655733 ACCTCAAAAACGTCGCACAG 59.344 50.000 0.00 0.00 0.00 3.66
3470 3694 0.375454 CACCTCAAAAACGTCGCACA 59.625 50.000 0.00 0.00 0.00 4.57
3471 3695 0.653636 TCACCTCAAAAACGTCGCAC 59.346 50.000 0.00 0.00 0.00 5.34
3472 3696 1.370609 TTCACCTCAAAAACGTCGCA 58.629 45.000 0.00 0.00 0.00 5.10
3473 3697 2.681152 ATTCACCTCAAAAACGTCGC 57.319 45.000 0.00 0.00 0.00 5.19
3474 3698 3.296628 CCAATTCACCTCAAAAACGTCG 58.703 45.455 0.00 0.00 0.00 5.12
3475 3699 3.049912 GCCAATTCACCTCAAAAACGTC 58.950 45.455 0.00 0.00 0.00 4.34
3476 3700 2.428890 TGCCAATTCACCTCAAAAACGT 59.571 40.909 0.00 0.00 0.00 3.99
3477 3701 3.090952 TGCCAATTCACCTCAAAAACG 57.909 42.857 0.00 0.00 0.00 3.60
3478 3702 4.692228 TCTTGCCAATTCACCTCAAAAAC 58.308 39.130 0.00 0.00 0.00 2.43
3479 3703 4.405358 ACTCTTGCCAATTCACCTCAAAAA 59.595 37.500 0.00 0.00 0.00 1.94
3480 3704 3.960102 ACTCTTGCCAATTCACCTCAAAA 59.040 39.130 0.00 0.00 0.00 2.44
3481 3705 3.318839 CACTCTTGCCAATTCACCTCAAA 59.681 43.478 0.00 0.00 0.00 2.69
3482 3706 2.886523 CACTCTTGCCAATTCACCTCAA 59.113 45.455 0.00 0.00 0.00 3.02
3483 3707 2.507484 CACTCTTGCCAATTCACCTCA 58.493 47.619 0.00 0.00 0.00 3.86
3484 3708 1.200948 GCACTCTTGCCAATTCACCTC 59.799 52.381 0.00 0.00 43.66 3.85
3485 3709 1.251251 GCACTCTTGCCAATTCACCT 58.749 50.000 0.00 0.00 43.66 4.00
3486 3710 3.800628 GCACTCTTGCCAATTCACC 57.199 52.632 0.00 0.00 43.66 4.02
3495 3719 0.383124 GAACAACGTCGCACTCTTGC 60.383 55.000 0.00 0.00 46.21 4.01
3496 3720 0.111704 CGAACAACGTCGCACTCTTG 60.112 55.000 0.00 0.00 37.22 3.02
3497 3721 0.248743 TCGAACAACGTCGCACTCTT 60.249 50.000 0.00 0.00 40.88 2.85
3498 3722 0.660595 CTCGAACAACGTCGCACTCT 60.661 55.000 0.00 0.00 40.88 3.24
3499 3723 1.767388 CTCGAACAACGTCGCACTC 59.233 57.895 0.00 0.00 40.88 3.51
3500 3724 2.300787 GCTCGAACAACGTCGCACT 61.301 57.895 0.00 0.00 40.88 4.40
3501 3725 2.167918 GCTCGAACAACGTCGCAC 59.832 61.111 0.00 0.00 40.88 5.34
3502 3726 3.391631 CGCTCGAACAACGTCGCA 61.392 61.111 0.00 0.00 40.88 5.10
3503 3727 1.941476 ATTCGCTCGAACAACGTCGC 61.941 55.000 6.88 0.00 40.88 5.19
3504 3728 0.246374 CATTCGCTCGAACAACGTCG 60.246 55.000 6.88 0.00 43.13 5.12
3505 3729 0.093026 CCATTCGCTCGAACAACGTC 59.907 55.000 6.88 0.00 43.13 4.34
3506 3730 1.897398 GCCATTCGCTCGAACAACGT 61.897 55.000 6.88 0.00 43.13 3.99
3507 3731 1.225745 GCCATTCGCTCGAACAACG 60.226 57.895 6.88 0.00 44.09 4.10
3508 3732 4.745549 GCCATTCGCTCGAACAAC 57.254 55.556 6.88 0.00 36.91 3.32
3517 3741 4.465512 CGCACCACAGCCATTCGC 62.466 66.667 0.00 0.00 37.98 4.70
3518 3742 2.741985 TCGCACCACAGCCATTCG 60.742 61.111 0.00 0.00 0.00 3.34
3519 3743 1.965930 TGTCGCACCACAGCCATTC 60.966 57.895 0.00 0.00 0.00 2.67
3520 3744 2.112928 TGTCGCACCACAGCCATT 59.887 55.556 0.00 0.00 0.00 3.16
3521 3745 2.669569 GTGTCGCACCACAGCCAT 60.670 61.111 0.00 0.00 35.38 4.40
3522 3746 4.168291 TGTGTCGCACCACAGCCA 62.168 61.111 1.52 0.00 40.30 4.75
3527 3751 0.385974 GCTCAAATGTGTCGCACCAC 60.386 55.000 7.38 0.97 32.73 4.16
3528 3752 1.840630 CGCTCAAATGTGTCGCACCA 61.841 55.000 7.38 0.00 32.73 4.17
3529 3753 1.154413 CGCTCAAATGTGTCGCACC 60.154 57.895 7.38 0.00 32.73 5.01
3530 3754 0.722469 CACGCTCAAATGTGTCGCAC 60.722 55.000 3.44 3.44 34.56 5.34
3531 3755 1.157257 ACACGCTCAAATGTGTCGCA 61.157 50.000 0.00 0.00 45.74 5.10
3532 3756 0.787787 TACACGCTCAAATGTGTCGC 59.212 50.000 0.72 0.00 45.74 5.19
3533 3757 3.513462 TTTACACGCTCAAATGTGTCG 57.487 42.857 0.72 0.08 45.74 4.35
3534 3758 5.022021 GCTATTTACACGCTCAAATGTGTC 58.978 41.667 0.72 0.00 45.74 3.67
3536 3760 4.342772 GGCTATTTACACGCTCAAATGTG 58.657 43.478 0.00 0.00 41.81 3.21
3537 3761 3.377172 GGGCTATTTACACGCTCAAATGT 59.623 43.478 0.00 0.00 0.00 2.71
3538 3762 3.376859 TGGGCTATTTACACGCTCAAATG 59.623 43.478 0.00 0.00 29.89 2.32
3539 3763 3.616219 TGGGCTATTTACACGCTCAAAT 58.384 40.909 0.00 0.00 29.89 2.32
3540 3764 3.006940 CTGGGCTATTTACACGCTCAAA 58.993 45.455 0.00 0.00 33.10 2.69
3541 3765 2.627945 CTGGGCTATTTACACGCTCAA 58.372 47.619 0.00 0.00 33.10 3.02
3542 3766 1.134521 CCTGGGCTATTTACACGCTCA 60.135 52.381 0.00 0.00 32.43 4.26
3543 3767 1.583054 CCTGGGCTATTTACACGCTC 58.417 55.000 0.00 0.00 0.00 5.03
3544 3768 0.180406 CCCTGGGCTATTTACACGCT 59.820 55.000 0.00 0.00 0.00 5.07
3545 3769 1.444917 GCCCTGGGCTATTTACACGC 61.445 60.000 30.42 0.00 46.69 5.34
3546 3770 2.702847 GCCCTGGGCTATTTACACG 58.297 57.895 30.42 0.00 46.69 4.49
3558 3782 4.764771 CACCCCATGTGGCCCTGG 62.765 72.222 0.00 4.51 41.52 4.45


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.